Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system von Chandler, James Angus, Lang, Jenna Morgan, Bhatnagar, Srijak, Eisen, Jonathan A, Kopp, Artyom

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Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota von Van Deynze, Allen, Zamora, Pablo, Delaux, Pierre-Marc, Heitmann, Cristobal, Jayaraman, Dhileepkumar, Rajasekar, Shanmugam, Graham, Danielle, Maeda, Junko, Gibson, Donald, Schwartz, Kevin D, Berry, Alison M, Bhatnagar, Srijak, Jospin, Guillaume, Darling, Aaron, Jeannotte, Richard, Lopez, Javier, Weimer, Bart C, Eisen, Jonathan A, Shapiro, Howard-Yana, Ané, Jean-Michel, Bennett, Alan B

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A simple, fast, and accurate method of phylogenomic inference von Wu, Martin, Eisen, Jonathan A

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Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance von Kembel, Steven W, Wu, Martin, Eisen, Jonathan A, Green, Jessica L

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Structure, variation, and assembly of the root-associated microbiomes of rice von Edwards, Joseph, Johnson, Cameron, Santos-Medellín, Christian, Lurie, Eugene, Podishetty, Natraj Kumar, Bhatnagar, Srijak, Eisen, Jonathan A., Sundaresan, Venkatesan

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An integrated pipeline for de novo assembly of microbial genomes von Tritt, Andrew, Eisen, Jonathan A, Facciotti, Marc T, Darling, Aaron E

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Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights von Pasolli, Edoardo, Truong, Duy Tin, Malik, Faizan, Waldron, Levi, Segata, Nicola

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Assembling the marine metagenome, one cell at a time von Woyke, Tanja, Xie, Gary, Copeland, Alex, González, José M, Han, Cliff, Kiss, Hajnalka, Saw, Jimmy H, Senin, Pavel, Yang, Chi, Chatterji, Sourav, Cheng, Jan-Fang, Eisen, Jonathan A, Sieracki, Michael E, Stepanauskas, Ramunas

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Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation von Rosado, Phillipe M., Leite, Deborah C. A., Duarte, Gustavo A. S., Chaloub, Ricardo M., Jospin, Guillaume, Nunes da Rocha, Ulisses, P. Saraiva, João, Dini-Andreote, Francisco, Eisen, Jonathan A., Bourne, David G., Peixoto, Raquel S.

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Best practices for scientific computing von Wilson, Greg, Aruliah, D A, Brown, C Titus, Chue Hong, Neil P, Davis, Matt, Guy, Richard T, Haddock, Steven H D, Huff, Kathryn D, Mitchell, Ian M, Plumbley, Mark D, Waugh, Ben, White, Ethan P, Wilson, Paul

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Accounting for alignment uncertainty in phylogenomics von Wu, Martin, Chatterji, Sourav, Eisen, Jonathan A

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Metabolic reconstruction for metagenomic data and its application to the human microbiome von Abubucker, Sahar, Segata, Nicola, Goll, Johannes, Schubert, Alyxandria M, Izard, Jacques, Cantarel, Brandi L, Rodriguez-Mueller, Beltran, Zucker, Jeremy, Thiagarajan, Mathangi, Henrissat, Bernard, White, Owen, Kelley, Scott T, Methé, Barbara, Schloss, Patrick D, Gevers, Dirk, Mitreva, Makedonka, Huttenhower, Curtis

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Drivers of bacterial β-diversity depend on spatial scale von Martiny, Jennifer B. H., Eisen, Jonathan A., Penn, Kevin, Allison, Steven D., Horner-Devine, M. Claire, DeLong, Edward F.

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Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response von Becker, Erin A, Seitzer, Phillip M, Tritt, Andrew, Larsen, David, Krusor, Megan, Yao, Andrew I, Wu, Dongying, Madern, Dominique, Eisen, Jonathan A, Darling, Aaron E, Facciotti, Marc T

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Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment von Castelle, Cindy J., Hug, Laura A., Wrighton, Kelly C., Thomas, Brian C., Williams, Kenneth H., Wu, Dongying, Tringe, Susannah G., Singer, Steven W., Eisen, Jonathan A., Banfield, Jillian F.

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Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes von Eisen, Jonathan A

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Amyotrophic lateral sclerosis: a long preclinical period? von Eisen, Andrew, Kiernan, Matthew, Mitsumoto, Hiroshi, Swash, Michael

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Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts von Martens, Eric C, Lowe, Elisabeth C, Chiang, Herbert, Pudlo, Nicholas A, Wu, Meng, McNulty, Nathan P, Abbott, D Wade, Henrissat, Bernard, Gilbert, Harry J, Bolam, David N, Gordon, Jeffrey I

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Metagenomic sequencing of an in vitro-simulated microbial community von Morgan, Jenna L, Darling, Aaron E, Eisen, Jonathan A

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Insights into the phylogeny and coding potential of microbial dark matter von Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip, Woyke, Tanja

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